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2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary Sloan
Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-19Finished integrating code that reads sample list from geno filesZachary Sloan
withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-18Merge branch 'master' of https://github.com/zsloan/genenetworkZachary Sloan
Conflicts: wqflask/base/webqtlConfigLocal.py wqflask/maintenance/gen_select_dataset.py wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
2013-07-18Added to installation notesZachary Sloan
Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)
2013-07-17Fixed gen_select_dataset.pyZachary Sloan
Appended redis installation info to notes
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-27Created a group manager page where user administrators can createZachary Sloan
groups of datasets to give/add read privileges to
2013-06-26Moved code creating DataSets object to a function in dataset.pyZachary Sloan
Added caching to creating DataSets object
2013-06-26Got code that creates DataSets object runningZachary Sloan
Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-06-25Added DataSets class to dataset.py that will be used to create list ofZachary Sloan
confidential datasets
2013-06-21Fixed bug where cursor was still being used in queryZachary Sloan
2013-06-20Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columnsLei Yan
in the correlation page weren't displaying
2013-06-19Merge branch 'flask' of git://github.com/zsloan/genenetwork into flaskLei Yan
Conflicts: wqflask/base/data_set.py
2013-06-19Changed QTL parameter name to "get_qtl_info" on trait.py andLei Yan
other places it's called, like search_results.py Added other trait info fields to correlation results page
2013-06-19Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary Sloan
Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
2013-06-13Merge /home/sam/gene into flaskZachary Sloan
Conflicts: wqflask/wqflask/templates/index_page.html Merging the code on Sam's branch onto my own
2013-06-13Fixed issue where too much memory was used as a result of creating aLei Yan
dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-12Fixed a couple issues with the template that caused theZachary Sloan
regular search results and show trait page to not display
2013-06-11Put trait info for correlation results page into a dictionary insteadLei Yan
of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-31Fixed the location column for the quick search pageZachary Sloan
Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
2013-05-30Rewrote some code in get_trait_info in dataset.pyLei Yan
Added spearman correlation to show_corr_results and template
2013-05-28Have correlation values appearing in a table in the templateLei Yan
Use scipy to calculate pearson correlation instead of old GN code
2013-05-23Worked on rewriting the function in data_set.py that gets the sampleLei Yan
values for each trait
2013-05-23Changed the way the query that gets sample ids is generatedLei Yan
2013-05-23Now calculates correlation values for traits, but not yet in templateLei Yan
2013-05-09Just added some print statements so I can show matrix/vectorZachary Sloan
shapes to Tony
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file
2013-04-09Nick's code works fine with human dataZachary Sloan
Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
2013-04-02Committing before splitting code that runs pylmm with plink filesZachary Sloan
and code that runs it with json
2013-04-02pylmm code is running for human data (plink .bed genotype files)Zachary Sloan
2013-03-19Searches work for the full access human datasets with mRNA assayZachary Sloan
searches, and the trait page can be loaded Need to get marker regression page working with human data now
2013-03-12Added the script generating probesetfreeze data matrix filesZachary Sloan
The script was created to regenerate a bad file for Evan
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-07Progress bar is now completely workingZachary Sloan
Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-02Created generate_probesetfreeze_file to create theZachary Sloan
"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-22Added some to notesZachary Sloan
2013-02-14Have marker regression results displaying as a scatterplot (just the points)Zachary Sloan
using d3.js
2013-02-13Fixed some bugs related to getting the marker regression page workingZachary Sloan
with Nick's code
2013-02-12Edited marker_regression.py and data_set.py to store the p-valuesZachary Sloan
and their corresponding markers to be used in the table of qtl results and other figures
2013-02-07Added code to marker_regression.py that creates the numpy arrays toZachary Sloan
pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited
2013-01-31Changed fd to kw in search_results.py, commented out some linesZachary Sloan
related to fd
2013-01-25Fixed a few bugs while trying to get the code running on the new serverZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.pyZachary Sloan
Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
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